DNA Fragment assembly - an NP-Hard problem - is one of the major steps in of DNA sequencing. Multiple strategies have been used for this problem, including greedy graph-based algorithms, deBruijn graphs, and the overlap-layout-consensus approach. This study focuses on the overlap-layout-consensus approach. Heuristics and computational intelligence methods are combined to exploit their respective benefits. These algorithm combinations were able to produce high quality results surpassing the best results obtained by a number of competitive algorithms specially designed and tuned for this problem on thirteen of sixteen popular benchmarks. This work also reinforces the necessity of using multiple search strategies as it is clearly observed that algorithm performance is dependent on problem instance; without a deeper look into many searches, top solutions could be missed entirely.
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http://dx.doi.org/10.1016/j.biosystems.2016.08.001 | DOI Listing |
STAR Protoc
January 2025
Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, TN, Italy; Department of Medicine, NYU Langone Medical Center, New York, NY 10016, USA. Electronic address:
Reduced expression of nucleolar genes induces stress and DNA damage. Here, we present a protocol to analyze DNA fragmentation at the single-cell level in Drosophila imaginal discs using an optimized alkaline comet assay. We describe steps for larvae development, tissue disaggregation, and single-cell dissociation.
View Article and Find Full Text PDFVet Med Sci
March 2025
Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey.
Understanding the genetic factors that influence meat yield is crucial due to the economic importance of average daily live weight gain (ADWG) in livestock. This study investigates the relationship between the c.*188G>A SNP in the 3'-UTR region of the akirin 2 gene and growth traits in Zavot cattle, focusing on the gene's role in muscle development.
View Article and Find Full Text PDFJ Occup Health
January 2025
Department of Environmental Health, University of Fukui School of Medical Science, Eiheiji, Fukui, Japan.
Objectives: Many chemicals have been used for industrial purposes, and some of them are carcinogenic to humans. However, their molecular mechanisms have not been well understood. Reactive oxygen species are generated from industrial chemicals and contribute to carcinogenesis.
View Article and Find Full Text PDFCurr Issues Mol Biol
January 2025
Laboratorio de Bioorgánica Tropical, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá 0824, Panama.
Considering that fungi display a great morphological, ecological, metabolic, and phylogenetic diversity, their taxonomic identification is extremely important because it helps us establish important information about each species and its possible biochemical and ecological roles. Traditionally, the identification of fungi at the species level has been carried out with molecular tools such as DNA sequencing, but it still represents a huge challenge today due to the heterogeneity of the fungal kingdom, making the task of identification a complex and difficult process. Biotyping, a type of chemotaxonomy, has been developed in the field of the identification/differentiation and classification of micro-fungi through tools such as mass spectrometry (MS).
View Article and Find Full Text PDFCurr Issues Mol Biol
January 2025
COSLINK, Songpa-gu, Seoul 05819, Republic of Korea.
Polydeoxyribonucleotide (PDRN) has emerged as a potent bioactive compound with proven efficacy in wound healing, tissue regeneration, and anti-inflammatory applications and is predominantly derived from salmonid gonads. However, this study presents a groundbreaking advancement by successfully extracting and characterizing PDRN from microbial sources, specifically , marking the first report to utilize microbial-, biome-, or -derived PDRN (L-PDRN). The findings demonstrate the enhanced biological properties of L-PDRN over traditional salmon-derived PDRN across several assays.
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